rpExtractSink

RetroPath2 sink generator. From a given SBML file, the tool will extract all the sink molecules and generate a csv file with the InChI structures. For each molecule, the InChI will be get from:

1. The local cache (rrCache), if available
2. The MetaNetX database from MIRIAM URLs (MetaNetX first)

Input

Required:

• input_sbml: (string) Path to the input SBML file

Optional:

• --remove-dead-end: (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites
• --compartment-id: (string, default: 'c') Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files
• --standalone: (boolean, default: False) If True, do not retrieve InChI from Internet
• --cache-dir: (string, default: None) Path to the cache directory

Output

• output_sbml: (string) Path to the output csv file

Installation Guide

Overview

rpextractsink depends on rplibs, which depends on cobra, which requires python-libsbml.
On Apple Silicon (arm64) macOS, python-libsbml is not available as a native Conda package.

Therefore, installation must be done using an Intel (osx-64) Conda environment under Rosetta.

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General case

conda install -c conda-forge rpextractsink

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Apple Silicon macOS (M1/M2/M3)

1. Install Rosetta 2

softwareupdate --install-rosetta --agree-to-license

2. Install rpLibs

CONDA_SUBDIR=osx-64 conda install -c conda-forge rpextractsink

Or with mamba:

CONDA_SUBDIR=osx-64 mamba install -c conda-forge rpextractsink

3. Persist platform setting

conda config --env --set subdir osx-64

5. Verify installation

python -c "import rpextractsink; print('rpextractsink installed successfully')"
python -c "import cobra; print(cobra.__version__)"

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Troubleshooting

Solver fails on Apple Silicon

Make sure you are using:

CONDA_SUBDIR=osx-64

Wrong architecture environment

Check:

conda config --show subdir

Expected output:

subdir: osx-64

Use

Function call from Python code

from rr_cache import rrCache
from rpextractsink import genSink

cache = rrCache()
sink = genSink(cache, args.input_sbml)

Run from CLI

python -m rpextractsink --help

Tests

Test can be run with the following commands:

Natively

python -m pytest

Authors

• Joan Hérisson
• Thomas Duigou, Melchior du Lac

License

This project is licensed under the MIT License - see the LICENSE file for details